############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NetPathMiner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NetPathMiner_1.43.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/NetPathMiner.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘NetPathMiner/DESCRIPTION’ ... OK * this is package ‘NetPathMiner’ version ‘1.43.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘NetPathMiner’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE package 'methods' is used but not declared * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE alpha: no visible global function definition for ‘col2rgb’ alpha: no visible global function definition for ‘rgb’ assignEdgeWeights : wt.func: no visible global function definition for ‘median’ assignEdgeWeights: no visible global function definition for ‘complete.cases’ assignEdgeWeights: no visible global function definition for ‘na.omit’ assignEdgeWeights : : no visible global function definition for ‘na.omit’ bpGetAnnFromXRef: no visible global function definition for ‘na.omit’ bpGetReferences: no visible global function definition for ‘setNames’ bpMetabolicL2: no visible global function definition for ‘setNames’ bpMetabolicL3: no visible global function definition for ‘setNames’ bpSignalingL3: no visible global function definition for ‘na.omit’ bpSplitComplex: no visible global function definition for ‘na.omit’ colorVertexByAttr: no visible global function definition for ‘palette’ colorVertexByAttr: no visible global function definition for ‘colorRampPalette’ drawLegend: no visible global function definition for ‘par’ drawLegend: no visible global function definition for ‘plot.new’ drawLegend: no visible global function definition for ‘strwidth’ drawLegend: no visible global function definition for ‘legend’ fetchAttribute: no visible global function definition for ‘na.omit’ fetchAttribute: no visible global function definition for ‘URLencode’ fetchAttribute: no visible global function definition for ‘setNames’ fetchAttribute : : no visible global function definition for ‘read.table’ getGeneSetNetworks: no visible global function definition for ‘setClass’ getGeneSetNetworks: no visible global function definition for ‘representation’ getPaths : : no visible global function definition for ‘head’ getPaths: no visible global function definition for ‘tail’ graph.sizes: no visible global function definition for ‘par’ makeReactionNetwork: no visible global function definition for ‘complete.cases’ pathClassifier: no visible binding for global variable ‘sd’ pathClassifier: no visible global function definition for ‘aggregate’ pathCluster: no visible binding for global variable ‘sd’ pathCluster: no visible global function definition for ‘aggregate’ plotAllNetworks: no visible global function definition for ‘palette’ plotAllNetworks: no visible global function definition for ‘par’ plotAllNetworks: no visible global function definition for ‘colorRampPalette’ plotClassifierROC: no visible global function definition for ‘palette’ plotClassifierROC: no visible global function definition for ‘layout’ plotClassifierROC: no visible global function definition for ‘na.omit’ plotClusterMatrix: no visible global function definition for ‘rainbow’ plotClusterMatrix: no visible global function definition for ‘image’ plotClusterMatrix: no visible global function definition for ‘axis’ plotClusterProbs: no visible global function definition for ‘rainbow’ plotClusterProbs: no visible global function definition for ‘matplot’ plotClusters: no visible global function definition for ‘rainbow’ plotClusters: no visible global function definition for ‘strwidth’ plotClusters: no visible global function definition for ‘layout’ plotClusters: no visible global function definition for ‘par’ plotClusters: no visible global function definition for ‘legend’ plotCytoscapeGML : col2hex: no visible global function definition for ‘rgb’ plotCytoscapeGML : col2hex: no visible global function definition for ‘col2rgb’ plotCytoscapeGML: no visible global function definition for ‘packageVersion’ plotNetwork: no visible global function definition for ‘palette’ plotNetwork: no visible global function definition for ‘par’ plotNetwork_internal: no visible global function definition for ‘palette’ plotNetwork_internal: no visible global function definition for ‘setNames’ plotPathClassifier: no visible global function definition for ‘palette’ plotPathClassifier: no visible global function definition for ‘par’ plotPathClassifier: no visible global function definition for ‘layout’ plotPathClassifier: no visible global function definition for ‘barplot’ plotPathClassifier: no visible global function definition for ‘abline’ plotPathClassifier: no visible global function definition for ‘points’ plotPathClassifier: no visible global function definition for ‘axis’ plotPathClassifier: no visible global function definition for ‘image’ plotPathClassifier: no visible global function definition for ‘cm.colors’ plotPathClassifier: no visible global function definition for ‘mtext’ plotPathClassifier: no visible global function definition for ‘lines’ plotPathCluster: no visible global function definition for ‘par’ plotPathCluster: no visible global function definition for ‘layout’ plotPathCluster: no visible global function definition for ‘barplot’ plotPathCluster: no visible global function definition for ‘abline’ plotPathCluster: no visible global function definition for ‘axis’ plotPathCluster: no visible global function definition for ‘image’ plotPathCluster: no visible global function definition for ‘cm.colors’ plotPathCluster: no visible global function definition for ‘mtext’ plotPathROC: no visible global function definition for ‘palette’ plotPathROC: no visible global function definition for ‘lines’ plotPathROC: no visible global function definition for ‘axis’ plotPathROC: no visible global function definition for ‘mtext’ plotPathROC: no visible global function definition for ‘legend’ plotPaths: no visible global function definition for ‘palette’ plotPaths: no visible global function definition for ‘par’ process.color: no visible global function definition for ‘colorRampPalette’ process.color: no visible global function definition for ‘setNames’ process.layout: no visible global function definition for ‘par’ processNetwork : : no visible global function definition for ‘ecdf’ reindexNetwork: no visible binding for global variable ‘head’ stdAttrNames : : no visible global function definition for ‘head’ stdAttrNames : : no visible global function definition for ‘setNames’ Undefined global functions or variables: URLencode abline aggregate axis barplot cm.colors col2rgb colorRampPalette complete.cases ecdf head image layout legend lines matplot median mtext na.omit packageVersion palette par plot.new points rainbow read.table representation rgb sd setClass setNames strwidth tail Consider adding importFrom("grDevices", "cm.colors", "col2rgb", "colorRampPalette", "palette", "rainbow", "rgb") importFrom("graphics", "abline", "axis", "barplot", "image", "layout", "legend", "lines", "matplot", "mtext", "par", "plot.new", "points", "strwidth") importFrom("methods", "representation", "setClass") importFrom("stats", "aggregate", "complete.cases", "ecdf", "median", "na.omit", "sd", "setNames") importFrom("utils", "URLencode", "head", "packageVersion", "read.table", "tail") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) plotClassifierROC.Rd:14: Lost braces 14 | item{Top}{ROC curves for the posterior probabilities (\code{mix\$posterior.probs}) | ^ checkRd: (-1) plotClassifierROC.Rd:14-17: Lost braces 14 | item{Top}{ROC curves for the posterior probabilities (\code{mix\$posterior.probs}) | ^ checkRd: (-1) plotClassifierROC.Rd:18: Lost braces 18 | item{Bottom}{The likelihood convergence history for the HME3M model. If the parameters | ^ checkRd: (-1) plotClassifierROC.Rd:18-19: Lost braces 18 | item{Bottom}{The likelihood convergence history for the HME3M model. If the parameters | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/NetPathMiner.Rcheck/00check.log’ for details.